Skip to another splice site:
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 5'  3'   		2  
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 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGCTGCCGCACCGCGCCCATGGAGGGCGTCGCCTTCTCCCCCGACGACCTCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTCgtaatccctcgattcctcccctactctattgtcattaattgttctttatgtatcggagtccatagcagcaatttgtgcggttaggaagctgttcatcctt...

Basic information

species Zea mays
transcript GRMZM5G862107_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G862107_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os03g20100.1 (Oryza sativa), 5'ss of exon 1
GCGCTGCCGCACCGCGCCCATGGAGGGCGTCGCCTTCTCCCCCGACGACCTCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTCgtaatccctcgattcctcccctactc-tattgtcattaattgttctt---------tatgtatcggagtccatagcagcaatttgtgcggttaggaagctgttcatcctt
||||||||||||||||||||||||||||||| ||||||| ||||| ||||||||| |||||||||||||||||||||| ||||| || |||||||| ||||||||||  |     |  || | ||| | || |  | ||| || |||         ||||    | |    |||| ||||||| ||||  |||  ||   |         
GCGCTGCCGCACCGCGCCCATGGAGGGCGTCTCCTTCTCGCCCGAGGACCTCGACTCCGCCGTCGAGTCCACCGACATCGACACCGATATCGGCTCACTCgtaatccaccccccgcaaccttcctcctgttcttctcaatcgtccttgctcgctcgtatgatgtgaaacagatagtagcaattggtgc--ttaaaaacaggc--------
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|74236428|gb|DT644342.1|DT644342
EST:     TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTC                         ATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
genomic: TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTCgtaatccctc ... gtgtctacagATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
EST: gi|148948413|gb|EC893930.2|EC893930
EST:     TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTC                         ATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
genomic: TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTCgtaatccctc ... gtgtctacagATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
EST: gi|148942422|gb|EC887441.2|EC887441
EST:     TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTC                         ATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
genomic: TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTCgtaatccctc ... gtgtctacagATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
EST: gi|37421987|gb|CF648698.1|CF648698
EST:     TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTC                         ATTAAAGGAACAGTATTTATGACTACCTCAAATGGGGCATATATCGACATC
genomic: TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTCgtaatccctc ... gtgtctacagATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
EST: gi|148967255|gb|EE018456.2|EE018456
EST:     TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTC                         ATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
genomic: TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTCgtaatccctc ... gtgtctacagATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
EST: gi|148950615|gb|EC896198.2|EC896198
EST:     TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTC                         ATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
genomic: TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTCgtaatccctc ... gtgtctacagATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
EST: gi|71327391|gb|DR800308.1|DR800308
EST:     TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTC                         ATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
genomic: TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTCgtaatccctc ... gtgtctacagATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
EST: gi|148973408|gb|EE024500.2|EE024500
EST:     TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTC                         ATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
genomic: TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTCgtaatccctc ... gtgtctacagATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
EST: gi|89758470|gb|DY687641.1|DY687641
EST:     TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTC                         ATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
genomic: TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTCgtaatccctc ... gtgtctacagATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
EST: gi|148969033|gb|EE019745.2|EE019745
EST:     TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTC                         ATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
genomic: TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTCgtaatccctc ... gtgtctacagATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
EST: gi|211456074|gb|FL267263.1|FL267263
EST:     TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTC                         ATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
genomic: TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTCgtaatccctc ... gtgtctacagATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
EST: gi|149073098|gb|EE161370.2|EE161370
EST:     TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTC                         ATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
genomic: TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTCgtaatccctc ... gtgtctacagATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
EST: gi|149085338|gb|EE174844.2|EE174844
EST:     TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTC                         ATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
genomic: TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTCgtaatccctc ... gtgtctacagATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
EST: gi|88756836|gb|DY540977.1|DY540977
EST:     TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTC                         ATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
genomic: TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTCgtaatccctc ... gtgtctacagATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
EST: gi|148968012|gb|EE019338.2|EE019338
EST:     TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTC                         ATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
genomic: TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTCgtaatccctc ... gtgtctacagATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
EST: gi|76918968|gb|DV167535.1|DV167535
EST:     TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTC                         ATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
genomic: TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTCgtaatccctc ... gtgtctacagATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
EST: gi|74240696|gb|DT648610.1|DT648610
EST:     TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTC                         ATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
genomic: TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTCgtaatccctc ... gtgtctacagATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
EST: gi|76915754|gb|DV166106.1|DV166106
EST:     TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTC                         ATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
genomic: TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTCgtaatccctc ... gtgtctacagATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
EST: gi|31364617|gb|CD448972.1|CD448972
EST:     TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTC                         ATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
genomic: TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTCgtaatccctc ... gtgtctacagATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
EST: gi|50339864|gb|CO534990.1|CO534990
EST:     TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTC                         ATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
genomic: TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTCgtaatccctc ... gtgtctacagATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
EST: gi|148972941|gb|EE023966.2|EE023966
EST:     TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTC                         ATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
genomic: TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTCgtaatccctc ... gtgtctacagATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
EST: gi|76280589|gb|DV020157.1|DV020157
EST:     TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTC                         ATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
genomic: TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTCgtaatccctc ... gtgtctacagATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
EST: gi|31558159|gb|CD527371.1|CD527371
EST:     TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTC                         ATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
genomic: TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTCgtaatccctc ... gtgtctacagATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
EST: gi|149110692|gb|EE190555.2|EE190555
EST:     TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTC                         ATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
genomic: TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTCgtaatccctc ... gtgtctacagATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
EST: gi|148954074|gb|EC899473.2|EC899473
EST:     TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTC                         ATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
genomic: TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTCgtaatccctc ... gtgtctacagATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
EST: gi|31354547|gb|CD438904.1|CD438904
EST:     TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTC                         ATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
genomic: TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTCgtaatccctc ... gtgtctacagATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
EST: gi|148962590|gb|EE013473.2|EE013473
EST:     TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTC                         ATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
genomic: TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTCgtaatccctc ... gtgtctacagATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
EST: gi|71769111|gb|DR967048.1|DR967048
EST:     TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTC                         ATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
genomic: TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTCgtaatccctc ... gtgtctacagATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
EST: gi|148997921|gb|EE035909.2|EE035909
EST:     TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTC                         ATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
genomic: TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTCgtaatccctc ... gtgtctacagATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
EST: gi|74241825|gb|DT649739.1|DT649739
EST:     TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTC                         ATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
genomic: TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTCgtaatccctc ... gtgtctacagATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
EST: gi|149080306|gb|EE169331.2|EE169331
EST:     TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTC                         ATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
genomic: TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTCgtaatccctc ... gtgtctacagATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
EST: gi|76932725|gb|DV173133.1|DV173133
EST:     TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTC                         ATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
genomic: TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTCgtaatccctc ... gtgtctacagATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
EST: gi|50327594|gb|CO522720.1|CO522720
EST:     TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTC                         ATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
genomic: TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTCgtaatccctc ... gtgtctacagATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
EST: gi|148987624|gb|EE031498.2|EE031498
EST:     TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTC                         ATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC
genomic: TCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTCgtaatccctc ... gtgtctacagATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 43 (downstream exon)
Score: 32

GCGCTGCCGCACCGCGCCCATGGAGGGCGTCGCCTTCTCCCCCGACGACCTCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTCgtaatccctc ... gtgtctacagATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATCCAATCCAAGTCTACTGCTTTTTTGCCCTTAGATGAGGCATGTCTTCTTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 295

GCGCTGCCGCACCGCGCCCATGGAGGGCGTCGCCTTCTCCCCCGACGACCTCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTCgtaatccctc ... gtgtctacagATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATCCAATCCAAGTCTACTGCTTTTTTGCCCTTAGATGAGGCATGTCTTCTTG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 22

GCGCTGCCGCACCGCGCCCATGGAGGGCGTCGCCTTCTCCCCCGACGACCTCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTCgtaatccctc ... gtgtctacagATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATCCAATCCAAGTCTACTGCTTTTTTGCCCTTAGATGAGGCATGTCTTCTTG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 77

GCGCTGCCGCACCGCGCCCATGGAGGGCGTCGCCTTCTCCCCCGACGACCTCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTCgtaatccctc ... gtgtctacagATTAAAGGAACAGTATTTATGACTACCTCAAATGGTGCATATATCGACATCCAATCCAAGTCTACTGCTTTTTTGCCCTTAGATGAGGCATGTCTTCTTG


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGCTGCCGCACCGCGCCCATGGAGGGCGTCGCCTTCTCCCCCGACGACCTCGACACCGCCGTCGAGTCCACCGACATAGACACGGAGATCGGCTCGCTCgtaatccctcgattcctcccctactctattgtcattaattgttctttatgtatcggagtccatagcagcaatttgtgcggttaggaagctgttcatcctt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctcccc